Disclosed herein are methods of preparing alkenes from beta-hydroxy or beta-sulfate carboxylic acid or carboxylic acid derivatives using thioesterase and optionally a sulfotransferase.
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1. A method for producing an alkene comprising:
(i) contacting a beta-hydroxy carboxylic acid or carboxylic acid derivative with a sulfonating reagent and a sulfotransferase (ST) under conditions that the ST mediates the formation of a beta-sulfate carboxylic acid or carboxylic acid derivative; and,
(ii) contacting the beta-sulfate carboxylic acid or carboxylic acid derivative with a thioesterase (TE) under conditions that the TE mediates decarboxylative elimination of the beta-sulfate carboxylic acid or carboxylic acid derivative to form the alkene;
wherein the ST and TE are tandem domains in the same polypeptide.
12. A method for producing an alkene comprising:
(i) contacting a beta-hydroxy carboxylic acid or carboxylic acid derivative with a sulfonating reagent and a sulfotransferase (ST), wherein the ST comprises SEQ ID NO: 4, or an enzymatically active fragment thereof which maintains the ST activity of SEQ ID NO: 4, under conditions that the ST mediates the formation of a beta-sulfate carboxylic acid or carboxylic acid derivative; and,
(ii) contacting the beta-sulfate carboxylic acid or carboxylic acid derivative with a thioesterase (TE), wherein the TE comprises an amino acid sequence that is at least 95% identical to SEQ ID NO: 3, or an enzymatically active fragment thereof which maintains the TE activity of SEQ ID NO: 3, under conditions that the TE mediates decarboxylative elimination of the beta-sulfate carboxylic acid or carboxylic acid derivative to form the alkene;
wherein the ST and TE are in separate polypeptides.
2. The method of
3. The method of
4. The method of
5. The method of
6. The method of
7. The method of
10. The method of
##STR00014##
wherein R is alkyl, heteroalkyl, cycloalkyl, aryl, heteroaryl, heterocycloalkyl, alkenyl, or alkynyl and can be optionally substituted with one or more of halo, alkyl, heteroalkyl, alkenyl, cycloalkyl, aryl, heteroaryl, heterocycloalkyl, nitro, cyano, amino, alkoxy, carboxy, carboxyalkyl, amido, thiol, hydroxy, and thioether;
R2 and R3 are each independently selected from the group consisting of hydrogen, alkyl, heteroalkyl, cycloalkyl, aryl, heteroaryl, heterocycloalkyl, alkenyl, or alkynyl and can be optionally substituted with one or more of halo, alkyl, heteroalkyl, alkenyl, cycloalkyl, aryl, heteroaryl, heterocycloalkyl, nitro, cyano, amino, alkoxy, carboxy, carboxyalkyl, amido, thiol, hydroxy, and thioether;
X is OH, SH, OR2, or SR2;
R1 is hydroxy or sulfate; and
R2 is optionally substituted alkyl, optionally substituted alkenyl, or a peptide.
11. The method of
13. The method of
14. The method of
15. The method of
16. The method of
18. The method of
##STR00015##
wherein R is alkyl, heteroalkyl, cycloalkyl, aryl, heteroaryl, heterocycloalkyl, alkenyl, or alkynyl and can be optionally substituted with one or more of halo, alkyl, heteroalkyl, alkenyl, cycloalkyl, aryl, heteroaryl, heterocycloalkyl, nitro, cyano, amino, alkoxy, carboxy, carboxyalkyl, amido, thiol, hydroxy, and thioether;
R2 and R3 are each independently selected from the group consisting of hydrogen, alkyl, heteroalkyl, cycloalkyl, aryl, heteroaryl, heterocycloalkyl, alkenyl, or alkynyl and can be optionally substituted with one or more of halo, alkyl, heteroalkyl, alkenyl, cycloalkyl, aryl, heteroaryl, heterocycloalkyl, nitro, cyano, amino, alkoxy, carboxy, carboxyalkyl, amido, thiol, hydroxy, and thioether;
X is OH, SH, OR2, or SR2;
R1 is hydroxy or sulfate; and
R2 is optionally substituted alkyl, optionally substituted alkenyl, or a peptide.
19. The method of
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The benefit of U.S. Provisional Application No. 61/227,987, filed Jul. 23, 2009 is claimed, and the disclosure of which is incorporated by reference herein in its entirety.
This invention was made with government support under DK042303 and CA108874 awarded by the National Institutes of Health. The Government has certain rights in the invention.
Curacin A is a mixed polyketide/non-ribosomal peptide with antimitotic properties produced by the marine cyanobacterium Lyngbya majuscula (4). The hybrid polyketide synthase (PKS)/non-ribosomal peptide synthase (NRPS) biosynthetic pathways that produces curacin A (5) contains numerous unique chemical steps, many of which have been previously investigated (1,3,6,22). The synthesis of a terminal alkene, instead of the carboxyl typical for this class of linear natural products, and the unique domain arrangement in the terminal PKS module are mysteries yet to be fully elucidated.
In CurM, the terminal module, a sulfotransferase (ST) and thioesterase (TE) domain follow the acyl carrier protein (ACP) (
The TE, although identifiable as a thioesterase, does not resemble any of the previously established fatty acid synthase (FAS), PKS or NRPS TE families (24). Many PKS offloading TEs have been studied to date including the TEs of the pikromycin synthase (Pik) (25,26) and erythromycin synthase (DEBS) (27) pathways. PKS offloading TEs typically perform either hydrolysis to produce a carboxylic acid or catalyze the attack of an intramolecular hydroxyl to form a macrolactone. These TEs are dimers, with two N-terminal alpha helices forming a lid-to-lid dimer interface, and adopt the α/β hydrolase fold characteristic of some serine hydrolases. Access to the classic nucleophile-His-acid catalytic triad active site is restricted by a narrow tunnel formed by a closed lid. Many PKS and NRPS pathways also include a second non-modular thioesterase called a TE II (in addition to an offloading TE, also known as TE I), which performs an editing function within the pathway. The curacin TE shows low similarity to sequences in all parts of the phylogenic tree (24), also pointing the need to more closely study curacin TE to understand its activity.
Disclosed herein are methods of preparing alkenes by decarboxylation of beta-sulfate carboxylic acids or carboxylic acid derivatives. More specifically, disclosed herein are methods of preparing alkenes by decarboxylative elimination to form the alkene.
Thus, in one aspect, provided herein is a method of contacting a beta-sulfate carboxylic acid or carboxylic acid derivative with a TE such that the TE mediates decarboxylative elimination of the beta-sulfate carboxylic acid or carboxylic acid derivative to form the alkene. In some cases, the TE comprises an amino acid sequence of SEQ ID NO: 3 or an enzymatically active fragment thereof which maintains the TE activity of SEQ ID NO: 3.
The method disclosed herein can further comprise contacting a beta-hydroxy carboxylic acid or carboxylic acid derivative with a sulfonating reagent and a sulfotransferase (ST) such that the ST mediates the formation of the beta-sulfate carboxylic acid or carboxylic acid derivative. In some cases, the ST comprises an amino acid sequence of SEQ ID NO: 4, or an enzymatically active fragment thereof which maintains the ST activity of SEQ ID NO: 4. The ST and TE can be in the same polypeptide or in different polypeptides.
The carboxylic acid derivative can comprise a carboxylic acid conjugated to an acyl carrier protein (ACP). In some cases, the ACP comprises an amino acid sequence SEQ ID NO: 5 or active fragment thereof. In various embodiments, the ACP and at least one of the TE and ST (e.g., ACP and TE and/or ACP and ST) are in the same polypeptide. In some cases, the ACP, TE and ST are all in the same polypeptide. In some embodiments, the ACP, TE and ST are all in the same polypeptide and that polypeptide comprises an amino acid sequence of SEQ ID NO: 1.
In some embodiments, the alkene is a terminal alkene. In various cases, the alkene has a structure of formula (II) and the beta-sulfate or beta-hydroxy carboxylic acid or carboxylic acid derivative has a structure of formula (I):
##STR00001##
wherein R is alkyl, heteroalkyl, cycloalkyl, aryl, heteroaryl, heterocycloalkyl, alkenyl, or alkynyl and can be optionally substituted with one or more of halo, alkyl, heteroalkyl, alkenyl, cycloalkyl, aryl, heteroaryl, heterocycloalkyl, nitro, cyano, amino, alkoxy, carboxy, carboxyalkyl, amido, thiol, hydroxy, and thioether;
- R2 and R3 are each independently selected from the group consisting of hydrogen, alkyl, heteroalkyl, cycloalkyl, aryl, heteroaryl, heterocycloalkyl, alkenyl, or alkynyl and can be optionally substituted with one or more of halo, alkyl, heteroalkyl, alkenyl, cycloalkyl, aryl, heteroaryl, heterocycloalkyl, nitro, cyano, amino, alkoxy, carboxy, carboxyalkyl, amido, thiol, hydroxy, and thioether;
- X is OH, SH, OR2, or SR2;
- R1 is hydroxy or sulfate; and
- R2 is optionally substituted alkyl, optionally substituted alkenyl, or a peptide. One example of a peptide of formula (I) is an ACP.
In another aspect, disclosed herein is an isolated crystalline form of a sulfotransferase (ST) polypeptide comprising an amino acid sequence of SEQ ID NO: 19, a space group P212121, unit cell parameters of a=45.8 Å, b=67.3 Å, c=118.0 Å, β=β=γ=90°, and one ST molecule in an asymmetric unit.
In yet another aspect, disclosed herein is an isolated crystalline form of a thioesterase (TE) polypeptide comprising an amino acid sequence of SEQ ID NO: 21, a space group P21, unit cell parameters of a=74.5 Å, b=86.9 Å, c=87.6 Å, α=γ=90°, β=90.8°, and four TE molecules in an asymmetric unit.
In still another aspect, disclosed herein is an isolated thioesterase (TE) polypeptide comprising an amino acid sequence that is greater than 75% identical to SEQ ID NO: 3 and exhibits TE activity. In some cases, the sequence is greater than 90%, greater than 95%, or greater than 98% identical to SEQ ID NO: 3. In a specific embodiment, the sequence is SEQ ID NO: 3.
Further disclosed herein is a polynucleotide encoding an isolated TE polypeptide disclosed herein. Also disclosed herein is a vector comprising such a polynucleotide, and a host cell comprising the polynucleotide or vector.
In another aspect, provided herein is a method of preparing a disclosed isolated TE polypeptide comprising culturing a host cell as disclosed herein and recovering the polypeptide.
In a further aspect, the invention provides an antibody specifically reactive with a polypeptide described herein.
Disclosed herein are methods of synthesizing an alkene, e.g., a terminal alkene, using natural or engineered enzymes. In particular, disclosed herein are methods of preparing an alkene from a beta-sulfate (OSO3−) carboxylic acid or carboxylic acid derivative by contacting the beta-sulfate carboxylic acid or carboxylic acid derivative with a thioesterase (TE) or fragment of a TE having TE enzymatic activity to form the alkene by decarboxylative elimination. The method can further comprise formation of the beta-sulfate carboxylic acid or carboxylic acid derivative by contacting a beta-hydroxy carboxylic acid or carboxylic acid derivative with a sulfotransferase (ST) or fragment of a ST having ST enzymatic activity to form the beta-sulfate carboxylic acid or carboxylic acid derivative thereof. Any beta-hydroxy (or sulfate) carboxylic acid A representative beta-hydroxy (sulfate) carboxylic acid or derivative thereof is illustrated in Formula (I), and can form an alkene of Formula (II):
##STR00002##
where R is alkyl, heteroalkyl, cycloalkyl, aryl, heteroaryl, heterocycloalkyl, alkenyl, or alkynyl, and optionally can be substituted with one or more of halo, alkyl, heteroalkyl, alkenyl, cycloalkyl, aryl, heteroaryl, heterocycloalkyl, nitro, cyano, amino, alkoxy, carboxy, carboxyalkyl, amido, thiol, hydroxy, and thioether;
- R2 and R3 are each independently selected from the group consisting of hydrogen, alkyl, heteroalkyl, cycloalkyl, aryl, heteroaryl, heterocycloalkyl, alkenyl, or alkynyl and can be optionally substituted with one or more of halo, alkyl, heteroalkyl, alkenyl, cycloalkyl, aryl, heteroaryl, heterocycloalkyl, nitro, cyano, amino, alkoxy, carboxy, carboxyalkyl, amido, thiol, hydroxy, and thioether;
- X is OH, SH, OR2, or SR2;
- R1 is hydroxy or sulfate (e.g., OSO3−); and
- R2 is optionally substituted alkyl, optionally substituted alkenyl, or a peptide, such as, e.g., an ACP.
“Decarboxylative elimination” used herein refers to elimination of a carboxylic acid or derivative thereof and optionally a beta-hydroxy (or sulfate) moiety to form an alkene. This process can be illustrated in the following reaction scheme:
##STR00003##
A “carboxylic acid derivative” as used herein refers to a moiety such as an ester, a thioester, an amide, or the like.
The term “alkyl” used herein refers to a saturated or unsaturated straight or branched chain hydrocarbon group of one to ten carbon atoms, including, but not limited to, methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, tert-butyl, n-hexyl, and the like. Alkyls of one to six carbon atoms are also contemplated. The term “alkyl” includes “bridged alkyl,” i.e., a bicyclic or polycyclic hydrocarbon group, for example, norbornyl, adamantyl, bicyclo[2.2.2]octyl, bicyclo[2.2.1]heptyl, bicyclo[3.2.1]octyl, or decahydronaphthyl. Alkyl groups optionally can be substituted, for example, with hydroxy (OH), halo, aryl, heteroaryl, cycloalkyl, heterocycloalkyl, and amino. It is specifically contemplated that in the analogs described herein the alkyl group consists of 1-40 carbon atoms, 1-25 carbon atoms, 1-15 carbon atoms, 1-12 carbon atoms, 1-10 carbon atoms, 1-8 carbon atoms, and 1-6 carbon atoms. “Heteroalkyl” is defined similarly as alkyl, except the heteroalkyl contains at least one heteroatom independently selected from the group consisting of oxygen, nitrogen, and sulfur.
As used herein, the term “cycloalkyl” refers to a cyclic hydrocarbon group, e.g., cyclopropyl, cyclobutyl, cyclohexyl, and cyclopentyl. “Heterocycloalkyl” is defined similarly as cycloalkyl, except the ring contains one to three heteroatoms independently selected from the group consisting of oxygen, nitrogen, and sulfur. Nonlimiting examples of heterocycloalkyl groups include piperdine, tetrahydrofuran, tetrahydropyran, dihydrofuran, morpholine, thiophene, and the like. Cycloalkyl and heterocycloalkyl groups can be saturated or partially unsaturated ring systems optionally substituted with, for example, one to three groups, independently selected from the group consisting of alkyl, alkyleneOH, C(O)NH2, NH2, oxo (═O), aryl, haloalkyl, halo, and OH. Heterocycloalkyl groups optionally can be further N-substituted with alkyl, hydroxyalkyl, alkylenearyl, or alkyleneheteroaryl.
The term “alkenyl” used herein refers to a straight or branched chain hydrocarbon group of two to thirty, or more, carbon atoms containing at least one carbon double bond including, but not limited to, 1-propenyl, 2-propenyl, 2-methyl-1-propenyl, 1-butenyl, 2-butenyl, and the like. “Alkynyl” refers to a straight or branched chain hydrocarbon group of two to thirty, or more, carbon atoms containing at least one carbon triple bond.
The term “halo” used herein refers to fluoro, chloro, bromo, or iodo.
The term “alkylene” used herein refers to an alkyl group having a substituent. For example, the term “alkylene aryl” refers to an alkyl group substituted with an aryl group. The alkylene group is optionally substituted with one or more substituent previously listed as an optional alkyl substituent. For example, an alkylene group can be —CH2CH2—.
As used herein, the term “alkenylene” is defined identical as “alkylene,” except the group contains at least one carbon-carbon double bond.
As used herein, the term “aryl” refers to a monocyclic or polycyclic aromatic group, preferably a monocyclic or bicyclic aromatic group, e.g., phenyl or naphthyl. Unless otherwise indicated, an aryl group can be unsubstituted or substituted with one or more, and in particular one to four groups independently selected from, for example, halo, alkyl, alkenyl, OCF3, NO2, CN, NC, OH, alkoxy, amino, CO2H, CO2alkyl, aryl, and heteroaryl. Exemplary aryl groups include, but are not limited to, phenyl, naphthyl, tetrahydronaphthyl, chlorophenyl, methylphenyl, methoxyphenyl, trifluoromethylphenyl, nitrophenyl, 2,4-methoxychlorophenyl, and the like.
As used herein, the term “heteroaryl” refers to a monocyclic or bicyclic ring system containing one or two aromatic rings and containing at least one nitrogen, oxygen, or sulfur atom in an aromatic ring. Unless otherwise indicated, a heteroaryl group can be unsubstituted or substituted with one or more, and in particular one to four, substituents selected from, for example, halo, alkyl, alkenyl, OCF3, NO2, CN, NC, OH, alkoxy, amino, CO2H, CO2alkyl, aryl, and heteroaryl. Examples of heteroaryl groups include, but are not limited to, thienyl, furyl, pyridyl, oxazolyl, quinolyl, thiophenyl, isoquinolyl, indolyl, triazinyl, triazolyl, isothiazolyl, isoxazolyl, imidazolyl, benzothiazolyl, pyrazinyl, pyrimidinyl, thiazolyl, and thiadiazolyl.
The term “alkoxy” used herein refers to straight or branched chain alkyl group covalently bonded to the parent molecule through an —O— linkage. Examples of alkoxy groups include, but are not limited to, methoxy, ethoxy, propoxy, isopropoxy, butoxy, n-butoxy, sec-butoxy, t-butoxy and the like.
The term “amino” as used herein refers to NR2, where R is independently hydrogen, optionally substituted alkyl, optionally substituted heteroalkyl, optionally substituted cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted aryl or optionally substituted heteroaryl. In some cases, R is independently hydrogen or alkyl. Non-limiting examples of amino groups include NH2 and N(CH3)2.
The term “amido” as used herein refers to —C(O)NH2, —C(O)NR2, —NRC(O)R or —NHC(O)H, where each R is independently hydrogen, optionally substituted alkyl, optionally substituted heteroalkyl, optionally substituted cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted aryl or optionally substituted heteroaryl. In some cases, the amido group is —NHC(O)alkyl or —NHC(O)H. A non-limiting example of an amido group is —NHC(O)CH3.
The term “carboxy” or “carboxyl” used herein refers to —COOH or its deprotonated form —COO−. Carboxyalkyl refers to optionally substituted alkyl or alkenyl groups having a carboxy moiety. Examples include, but are not limited to, —CH2COOH, —CH2CH(COOH)CH3, and CH2CH2CH2COOH.
The TE, ST, and/or ACP can be in separate polypeptides or in the same polypeptide. For example, CurM (SEQ ID NO: 1—amino acid sequence; SEQ ID NO: 2—nucleic acid sequence) comprises a TE, ST, and ACP domain at residues 1929 to 2211 (TE) (SEQ ID NO: 3); 1622 to 1905 (ST) (SEQ ID NO: 4); and 1504 to 1592 (ACP) (SEQ ID NO: 5).
It is contemplated that longer or indeed shorter peptides of TE, ST, and/or ACP also may prove useful. Thus, also contemplated are peptides that comprise at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90 or more amino acids from the TE, ST, and/or ACP peptide added to its N-terminus. For example, the amino acid at position 1928 of SEQ ID NO: 1, 1621 of SEQ ID NO:1, and/or 1503 of SEQ ID NO:1 could be added to a peptide described herein, if the addition of 1 amino acid to the N-terminus of a peptide sequence described herein is desired. Similarly, the amino acids from any one of positions 1502, 1501, 1500, 1499, 1498, 1497, 1496, 1495, 1494, 1489, or 1484 to 1503 of SEQ ID NO: 1 could be added to a peptide described herein if the addition of 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, or 20 amino acids, respectively, to the N-terminus of the ACP peptide is desired. The amino acids from any one of positions 1620, 1619, 1618, 1617, 1616, 1615, 1614, 1613, 1612, 1607, or 1602 to 1621 of SEQ ID NO: 1 could be added to a peptide described herein if the addition of 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, or 20 amino acids, respectively, to the N-terminus of the ST peptide is desired. The amino acids from any one of positions 1927, 1926, 1925, 1924, 1923, 1922, 1921, 1920, 1919, 1914, or 1909 to 1928 of SEQ ID NO: 1 could be added to a peptide described herein if the addition of 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, or 20 amino acids, respectively, to the N-terminus of the TE peptide is desired.
In some embodiments, a peptide described herein comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90 or more amino acids added to its C-terminus. These amino acids can be from the native CurM sequence or can be unnatural additional amino acids added that still at least substantially maintain the enzymatic activity of the ACP, ST, and/or TE. For example, the amino acid at position 1593 of SEQ ID NO: 1 and/or 1906 of SEQ ID NO:1 could be added to a peptide described herein to the ACP and/or ST peptide, respectively. Similarly, the amino acids from 1593 to any one of positions 1594, 1595, 1596, 1597, 1598, 1599, 1600, 1601, 1602, 1607, or 1612 of SEQ ID NO: 1 could be added to a peptide described herein if the addition of 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, or 20 amino acids, respectively, to the C-terminus of the ACP peptide is desired. The amino acids from 1906 to any one of positions 1607, 1908, 1909, 1910, 1911, 1912, 1913, 1914, 1915, 1920, or 1925 of SEQ ID NO: 1 could be added to a peptide described herein if the addition of 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, or 20 amino acids, respectively, to the C-terminus of the ST peptide is desired. Since the CurM protein (SEQ ID NO: 1) ends with the TE peptide, non-native amino acids can be added to the TE peptide C-terminus, e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, or 20 amino acids.
In some embodiments, the addition of amino acids to both the N- and C-termini of a peptide described herein is contemplated.
The term “polypeptide” as used herein, refers to amino acids joined to each other by peptide bonds or modified peptide bonds, i.e., peptide isosteres, and may contain modified amino acids other than the 20 gene-encoded amino acids. The polypeptides may be modified by either natural processes, such as post-translational processing, or by chemical modification techniques which are well known in the art. Modifications can occur anywhere in the polypeptide, including the peptide backbone, the amino acid side-chains and the amino or carboxyl termini. It will be appreciated that the same type of modification may be present in the same or varying degrees at several sites in a given polypeptide. Also a given polypeptide may have many types of modifications. Modifications can include, but are not limited to, acetylation, acylation, ADP-ribosylation, amidation, covalent attachment of flavin, covalent attachment of a heme moiety, covalent attachment of a nucleotide or nucleotide derivative, covalent attachment of a lipid or lipid derivative, covalent attachment of a phosphytidylinositol, cross-linking cyclization, disulfide bond formation, demethylation, formation of covalent cross-links, formation of cysteine, formation of pyroglutamate, formylation, gamma-carboxylation, glycosylation, GPI anchor formation, hydroxylation, iodination, methylation, myristolyation, oxidation, pergylation, proteolytic processing, phosphorylation, prenylation, racemization, selenoylation, sulfation, and/or transfer-RNA mediated addition of amino acids to protein such as arginylation. (See Proteins—Structure and Molecular Properties 2nd Ed., T. E. Creighton, W. H. Freeman and Company, New York (1993); Posttranslational Covalent Modification of Proteins, B. C. Johnson, Ed., Academic Press, New York, pp. 1-12 (1983)).
As used herein, the term “isolated” means that the material is removed from its original environment (e.g., the natural environment if it is naturally occurring). For example, a naturally occurring polynucleotide or polypeptide present in a living animal is not isolated, but the same polynucleotide or polypeptide, separated from some or all of the coexisting materials in the natural system, is isolated. Such polynucleotides could be part of a vector and/or such polynucleotides or polypeptides could be part of a composition, and still be isolated in that such vector or composition is not part of its natural environment.
As used herein, the term “purified” does not require absolute purity; rather, it is intended as a relative definition. Individual nucleic acids obtained from a library have been conventionally purified to electrophoretic homogeneity. The sequences obtained from these clones could not be obtained directly either from the library or from total human DNA. The purified nucleic acids of the invention have been purified from the remainder of the genomic DNA in the organism by at least 104-106 fold. However, the term “purified” also includes nucleic acids that have been purified from the remainder of the genomic DNA or from other sequences in a library or other environment by at least one order of magnitude, typically two or three orders, and more typically four or five orders of magnitude.
As used herein, the term “recombinant” means that the nucleic acid is adjacent to “backbone” nucleic acid to which it is not adjacent in its natural environment. Additionally, to be “enriched” the nucleic acids will represent 5% or more of the number of nucleic acid inserts in a population of nucleic acid backbone molecules. Backbone molecules according to the invention include nucleic acids such as expression vectors, self-replicating nucleic acids, viruses, integrating nucleic acids, and other vectors or nucleic acids used to maintain or manipulate a nucleic acid insert of interest. Typically, the enriched nucleic acids represent 15% or more of the number of nucleic acid inserts in the population of recombinant backbone molecules. More typically, the enriched nucleic acids represent 50% or more of the number of nucleic acid inserts in the population of recombinant backbone molecules. In a one embodiment, the enriched nucleic acids represent 90% or more of the number of nucleic acid inserts in the population of recombinant backbone molecules.
“Recombinant” polypeptides or proteins refer to polypeptides or proteins produced by recombinant DNA techniques; i.e., produced from cells transformed by an exogenous DNA construct encoding the desired polypeptide or protein or produced from a DNA construct by enzymes (transcribed by an RNA polymerase and translated by ribosomes, tRNAs and accessory proteins outside a cell). “Synthetic” polypeptides or protein are those prepared by chemical synthesis. Solid-phase chemical peptide synthesis methods can also be used to synthesize the polypeptide or fragments of the invention. Such method have been known in the art since the early 1960's (Merrifield, R. B., J. Am. Chem. Soc., 85:2149-2154, 1963) (See also Stewart, J. M. and Young, J. D., Solid Phase Peptide Synthesis, 2 ed., Pierce Chemical Co., Rockford, Ill., pp. 11-12)) and have recently been employed in commercially available laboratory peptide design and synthesis kits (Cambridge Research Biochemicals). Such commercially available laboratory kits have generally utilized the teachings of H. M. Geysen et al, Proc. Natl. Acad. Sci., USA, 81:3998 (1984) and provide for synthesizing peptides upon the tips of a multitude of “rods” or “pins” all of which are connected to a single plate. When such a system is utilized, a plate of rods or pins is inverted and inserted into a second plate of corresponding wells or reservoirs, which contain solutions for attaching or anchoring an appropriate amino acid to the pin's or rod's tips. By repeating such a process step, i.e., inverting and inserting the rod's and pin's tips into appropriate solutions, amino acids are built into desired peptides. In addition, a number of available FMOC peptide synthesis systems are available. For example, assembly of a polypeptide or fragment can be carried out on a solid support using an Applied Biosystems, Inc. Model 431A automated peptide synthesizer. Such equipment provides ready access to the peptides of the invention, either by direct synthesis or by synthesis of a series of fragments that can be coupled using other known techniques.
A promoter sequence is “operably linked to” a coding sequence when the RNA polymerase that initiates transcription at the promoter will transcribe the coding sequence into mRNA.
“Plasmids” are designated by a lower case p preceded and/or followed by capital letters and/or numbers. The starting plasmids herein are either commercially available, publicly available on an unrestricted basis, or can be constructed from available plasmids in accord with published procedures. In addition, equivalent plasmids to those described herein are known in the art and will be apparent to the ordinarily skilled artisan.
“Digestion” of DNA refers to catalytic cleavage of the DNA with a restriction enzyme that acts only at certain sequences in the DNA. The various restriction enzymes used herein are commercially available and their reaction conditions, cofactors and other requirements were used as would be known to the ordinarily skilled artisan. For analytical purposes, typically 1 g of plasmid or DNA fragment is used with about 2 units of enzyme in about 201 of buffer solution. For the purpose of isolating DNA fragments for plasmid construction, typically 5 to 50 g of DNA are digested with 20 to 250 units of enzyme in a larger volume. Appropriate buffers and substrate amounts for particular restriction enzymes are specified by the manufacturer. Incubation times of about 1 hour at 37 C are ordinarily used, but may vary in accordance with the supplier's instructions. After digestion the gel electrophoresis may be performed to isolate the desired fragment.
“Oligonucleotide” refers to either a single stranded polydeoxynucleotide or two complementary polydeoxynucleotide strands which may be chemically synthesized. Such synthetic oligonucleotides have no 5′ phosphate and thus will not ligate to another oligonucleotide without adding a phosphate with an ATP in the presence of a kinase. A synthetic oligonucleotide will ligate to a fragment that has not been dephosphorylated.
The phrase “substantially identical” in the context of two nucleic acid sequences or polypeptides, refers to two or more sequences that have greater than 60%, greater than 70%, greater than 80%, greater than 90%, greater than 91%, greater than 92%, greater than 93%, greater than 94%, greater than 95%, greater than 96%, greater than 97%, greater than 98%, or greater than 99% nucleotide or amino acid residue identity, when compared and aligned for maximum correspondence, as measured using one of the known sequence comparison algorithms or by visual inspection. The substantial identity can exists over a region of at least about 100 residues, and in some cases, the sequences are substantially identical over at least about 150-200 residues. In some embodiments, the sequences are substantially identical over the entire length of the nucleotide or polypeptide.
Additionally a “substantially identical” amino acid sequence is a sequence that differs from a reference sequence by one or more conservative or non-conservative amino acid substitutions, deletions, or insertions, particularly when such a substitution occurs at a site that is not the active site of the molecule, and provided that the polypeptide essentially retains its functional properties. A conservative amino acid substitution, for example, substitutes one amino acid for another of the same class (e.g., substitution of one hydrophobic amino acid, such as isoleucine, valine, leucine, or methionine, for another, or substitution of one polar amino acid for another, such as substitution of arginine for lysine, glutamic acid for aspartic acid or glutamine for asparagine). One or more amino acids can be deleted, for example, from a haloalkane dehalogenase polypeptide, resulting in modification of the structure of the polypeptide, without significantly altering its biological activity. Modified polypeptide sequences of the invention can be assayed for haloalkane dehalogenase biological activity by any number of methods, including contacting the modified polypeptide sequence with an haloalkane dehalogenase substrate and determining whether the modified polypeptide decreases the amount of specific substrate in the assay or increases the bioproducts of the enzymatic reaction of a functional haloalkane dehalogenase polypeptide with the substrate.
“Fragments” as used herein are a portion of a naturally occurring or recombinant protein that can exist in at least two different confirmations. Fragments can have the same or substantially the same amino acid sequence as the naturally occurring protein. “Substantially the same” means that an amino acid sequence is largely, but not entirely, the same, but retains at least one functional activity of the sequence to which it is related. In general two amino acid sequences are “substantially the same” or “substantially homologous” if they are greater than about 50%, but more typically greater than about 70%, greater than about 85%, or greater than about 90% identical. Fragments that have different three-dimensional structures as the naturally occurring protein are also included. An example of this, is a “pro-form” molecule, such as a low activity proprotein that can be modified by cleavage to produce a mature enzyme with significantly higher activity.
“Enzymatically active fragment” refers to a fragment of, e.g., TE, ST, and ACP, which retains some or all of the enzymatic activity of the full TE, ST, and/or ACP sequence. The activity of the fragment can be for example, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or at least 95% the activity of the original sequence.
CurM
CurM was sequenced and additional parts of the 3′ flanking region of the cur cluster in another cosmid (pLM14), from the L. majuscula genomic DNA library (14), and compared the data with those from a L. majuscula genome sequencing project. It revealed that the 3′ end of the deposited cur gene cluster (5) starting from the middle of curM TE region was indeed chimeric. The revised gene cluster lacks “curN”, and a complete TE domain is encoded by the 3′ end of curM (5). The adjacent downstream genes show high homology to tRNA 2-selenouridine synthase (ATPase) and adenylate/guanylate cyclase (Cy), and are not likely involved in curacin biosynthesis (
To biochemically assess the ST-TE mediated chain termination process, CurM ACP, ST and TE were cloned and overexpressed as soluble single domain constructs. ST was eluted as a monomer and TE as a dimer from an analytical size-exclusion column. ACP was overexpressed in the apo form in order to generate ACP-linked substrates. A simplified model substrate, 3-hydroxy-5-methoxytetradecanoyl-CoA (1-CoA,
With the soluble enzymes and model substrates in hand, the key issues in curacin A chain termination were investigated, including, 1) whether the sulfonated carboxylic acid (2,
Polyketide Chain Release by TE hydrolysis.
First, it was investigated whether the CurM TE exhibits canonical hydrolysis activity to cleave the thioester bond. (3S)-1-ACP and (3R)-1-ACP were prepared as the TE substrates to test its stereoselectivity for the β-hydroxyl group. The reactions were analyzed by reverse-phase HPLC, and the separated ACP fractions were examined by Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) and infrared multiphoton dissociation (IRMPD) (16) techniques. In addition, the chain-release products were detected by LC-MS and confirmed by co-injection with authentic standards. Both of the acyl groups were found to be hydrolyzed from (3S)-1-ACP and (3R)-1-ACP with low efficiency (
On-Assembly-Line Sulfonation by CurM ST.
Based on the known mechanism of ST enzyme function, CurM ST was predicted to bind to PAPS, and transfer a sulfonate moiety to the β-hydroxyl group of the intermediate tethered to or released from CurM ACP (
Terminal Olefin Formation via Decarboxylative Elimination in the Cur Pathway.
With the order of the ST and TE reactions established for the acyl-ACP intermediate, the next investigation was to couple the two reactions in one pot. When (3R)-1-ACP was treated with both ST and TE, complete release of the acyl chain from CurM ACP was observed by HPLC (
Next, experiments were performed to assess whether the proposed sulfonated intermediate (3R)-2 (
Disclosed herein are the biochemical reactions for the natural product biosynthesis of curacin A. A functional ST is inserted into the CurM PKS chain termination module leading to a unique series of on-assembly-line reactions. Specifically, these catalytic events transform the β-hydroxyl of the penultimate chain elongation intermediate into a β-sulfate, an excellent leaving group that is positioned chemically to facilitate decarboxylative elimination in the presence of the terminal carboxylate following TE-mediated hydrolysis of the acyl-thioester (
The significant levels of (3R)-2 (greater than 50%) as a product of the TE reaction from model substrate (3R)-1-ACP (
Finally, a highly similar strategy of terminal olefin formation occurs in the mevalonate pathway for isoprenoid biosynthesis (18). Specifically, mevalonate-5-diphosphate decarboxylase (MDD), along with mevalonate kinase and mevalonate-5-phosphate kinase catalyze a decarboxylative elimination reaction by first converting a β-hydroxyl group into a phosphate leaving group (
Structural Insights into Terminal Alkene Formation by the Thioesterase in the Curacin A Biosynthetic Pathway
The crystal structure of CurM TE was determined to 1.7 Å. CurM TE has the expected α/β hydrolase fold but differs from other offloading TEs in lid structure and dimer interface position, which results in an open-cleft active site. Comparison with uncharacterized sequences of putative tandem ST-TE domains with presumably similar activity reveals dense conservation within the cleft. A model of the predicted acyl enzyme intermediate shows a conserved Arg205, which may confer specificity to TE for the β-sulfate, a prediction that is supported by site-directed mutagenesis studies.
Using a simplified analogue, 3-hydroxy-5-methoxytetradecanoyl-ACP, of the penultimate pathway intermediate, it has been recently demonstrated that offloading and terminal bond formation starts with the ST sulfating the β-hydroxyl group of the intermediate using the sulfate donor PAPS (28) (
In order to understand this novel decarboxylation and desulfation activity, CurM TE was crystallized and its three-dimensional structure was determined. Significant differences from the PKS offloading TEs were observed, especially in the lid region. Using information from the structure, and sequence alignments, a prediction of β-sulfate recognition was developed. Point mutations were made and the activity in these mutants was tested to lend support to the initial prediction, giving a mechanism for the decarboxylation and desulfation activity and specificity towards the sulfated β-hydroxyl.
Structure Determination
Since the TE is a single domain at the terminus of a larger polypeptide (CurM), the N-terminal boundary of the TE domain was ambiguous. Constructs were made with three different N-termini with the addition of the fusion protein Mocr necessary to obtain a useable yield of soluble protein. The construct starting at amino acid 1929 of CurM yielded crystals with three amino acids (SNA) added to the N-terminus (SEQ ID NO: 21). The structure was solved by SAD phasing using selenomethionyl CurM TE to 2.2 Å. A native dataset of the same crystal form was collected to 1.7 Å and was used for refinement (Table 1). The CurM TE crystal structure is deposited in the public database for three-dimensional structures of biological macromolecules (Protein Data Bank, PDB, http://www.rcsb.org) and is available with the accession code 2H7X.
TABLE 1
CurM TE (SeMet)
CurM TE (native)
Diffraction Data
Space group
P21
P21
a, b, c (Å)
74.1, 86.9, 87.1
74.5, 86.9, 87.6
α, β, γ (°)
90, 90.4, 90
90, 90.8, 90
Wavelength (Å)
0.97948
1.0332
Resolutiona (Å)
50-2.14
(2.22-2.14)
50-1.68
(1.74-1.68)
<I/σI>
16.3
(5.5)
18.1
(2.1)
Rsymm
0.113
(0.362)b
0.059
(0.384)
Completeness
99.5
(99.9)
90.2
(49.8)
Average redundancy
6.4
(6.3)
3.4
(2.0)
Unique reflections
60,509
127,036
Total reflections
784700
808,263
Refinement
Data range (Å)
47.46-2.14
34.82-1.68
No. reflections
57,064
108,716
Rwork/Rfreec
0.188/0.237
0.178/0.221
RMS deviations
Bonds (Å)
0.013
0.013
Angles (°)
1.351
1.331
B-factors (Å2)
Protein
17.9
26.8
Water
22.5
39.6
Ramachandran
allow
99.90%
99.60%
outliers
0.10%
0.40%
Protein Atoms
8177
8349
Water Molecules
455
1119
The CurM TE structure adopts the α/β hydrolase fold with residues 1-128 and 217-283 of SEQ ID NO: 21 comprising the core domain and residues 136-204 comprising the lid (
Despite its sulfotransferase (ST) catalytic activity, the CurM ST sequence could not be mapped onto any known ST structure due to low sequence identity. The CurM ST was excised from CurM as an individual domain comprising residues 1598-1917 of SEQ ID NO:1 and a three amino acid addition to the N-terminus—SNA (at positions-3, -2, and -1) (SEQ ID NO:19, renumbered as -3-320 for purposes of the description in this paragraph). Single amino acid substitutions of Gln259Ala and Lys260Ala (SEQ ID NO: 20) were engineered to reduce surface entropy and enable crystallization of the monomeric protein, and the 1.6-Å crystal structure of the recombinant ST was determined (Table 2). The core of CurM ST, representing only about 60% of the structure, has a fold similar to those of other STs, but the CurM ST has additional loops and helices in unique positions surrounding the core (
TABLE 2
Diffraction Data
Space group
P212121
a, b, c (Å)
45.8 Å, 67.3 Å, 118.0 Å
α, β, γ (°)
90, 90, 90
Wavelength (Å)
1.0332
Data rangea (Å)
50-1.62
(1.68-1.62)
Avg. I/σI
17.5
(4.9)
Rsymm
0.074
(0.375)
Completeness (%)
98.5
(89.6)
Average redundancy
6.6
(5.9)
Unique reflections
46,830
Refinement
Data range (Å)
36.34-1.62
No. reflections
42,456
Rwork/Rfree
0.185/0.205
RMS deviations
Bonds (Å)
0.012
Angles (°)
1.416
B-factors (Å2)
Protein
15.5
Water
24.7
Ramachandran
Allowed
100.0%
Outliers
0.0%
Protein atoms (#)
2281
Water sites (#)
187
Ligands & ions (#)
15
Comparison to other Offloading TEs
CurM TE has similar secondary structure to other PKS offloading TEs in the core, but significant differences in secondary structure arrangement exist in the lid region (
Despite these differences, the position of the catalytic triad in the active site is well conserved compared to the PKS TEIs, but with the replacement of the Asp from the PKS TEIs with Glu in CurM TE (
##STR00004##
The predicted sulfated tetrahedral intermediate was modeled into the crystal structure using knowledge of nucleophile-His-acid active site catalysis and geometry and the affinity label from Pik TE (25) as a guide (
Comparison with Conserved ACP-ST-TE Sequences
When blasting the ACP-ST-TE amino acid sequence from CurM into the NCBI protein database, five other sequences were identified with 51-33% identity with CurM ACP-ST-TE (
Aligning these five sequences with CurM results in 51%-32% identity (
Activity of Point Mutants
The activity of these mutants was tested using the same assay described previously (28). A one-pot reaction was used where CurM ACP was loaded with a synthesized substrate mimic (
TABLE 3
% Activity
WT
100
R205Q
1.8 ± 0.3
R205E
2.3 ± 2.1
R205A
6.1 ± 3.1
N267A
38.4 ± 3.1
N211A
54.7 ± 1.8
H266R
1.4 ± 0.2
NO TE
0
These studies result in an overall scheme of double bond formation where the β-sulfate group interacts with Arg205 to bind and react with CurM TE. It is important to note that the wild type and mutants do not react with the non-sulfated substrate, indicating CurM TE is selective for a β-sulfate group. This selection could come from the β-sulfate acting as a “handle” which R205 can use to position the substrate for catalysis. The open active site may not have sufficient specificity to allow for non-sulfated substrates to be positioned for catalysis, resulting in the observed inactivity. R205 could also plays a role in driving the concerted release of CO2 and SO4−2 instead of the production of a carboxylic acid as would be seen in a canonical PKS TE I. The production of the sulfated carboxylic acid as well as the terminal alkene product were detected (28), indicating that in the system tested, at least part of the catalysis proceeds via the carboxylic acid. The analogous carboxylate and sulfated curacin product was never detected as being produced from L. majuscula, on the experimental detection of the carboxylated and sulfated product may be an off-pathway result of the experimental conditions.
CurM TE represents a new branch of the thioesterase family, optimized to work in concert with a ST to create a terminal double bond. There are already five other cases in the protein database where this type of TE appears. It may be that other organisms that have been found to produce hydrocarbons with terminal alkenes, such as Botryococcus braunii (44) may use this same ST-TE offloading strategy. This ability to create a terminal double bond could have applications in introducing diversity into natural products through combinatorial biosynthesis of FAS and PKS pathways, or producing hydrocarbons with terminal alkenes for possible use as a biofuel.
CurM TE has been found to have an intact catalytic triad active site, which is much more open compared to other studied PKS TEs. The unique lid arrangement and dimer interface facilitates the open-cleft surrounding the active site. High sequence conservation within the active site cleft point to its importance in CurM TE specificity and activity. Specificity is invoked through R205 guiding the β-sulfated substrate into position for catalysis in a cleft that is excessively for correct positioning of non-sulfated substrates.
Recombinant Production of Proteins
DNA encoding a polypeptide disclosed herein may be isolated and sequenced from a host cell secreting the protein using conventional procedures. Sequence determination will generally require isolation of at least a portion of the gene or cDNA of interest. Usually this requires cloning the DNA or, preferably, mRNA (i.e., cDNA) encoding the polypeptide. Cloning is carried out using standard techniques (see, e.g., Sambrook et al. (1989) Molecular Cloning: A Laboratory Guide, Vols 1-3, Cold Spring Harbor Press, which is incorporated herein by reference). For example, a cDNA library may be constructed by reverse transcription of polyA+ mRNA, preferably membrane-associated mRNA, and the library screened using probes specific for human immunoglobulin polypeptide gene sequences. Nucleotide probe reactions and other nucleotide hybridization reactions are carried out at conditions enabling the identification of polynucleotides that hybridize to each other under specified conditions.
One exemplary set of conditions is as follows: stringent hybridization at 42° C. in 50% formamide, 5×SSC, 20 mM Na.PO4, pH 6.8; and washing in 1×SSC at 55° C. for 30 minutes. Formulae for calculating equivalent hybridization conditions and/or selecting other conditions to achieve a desired level of stringency are well known. It is understood in the art that conditions of equivalent stringency can be achieved through variation of temperature and buffer, or salt concentration as described Ausubel, et al. (Eds.), Protocols in Molecular Biology, John Wiley & Sons (1994), pp. 6.0.3 to 6.4.10. Modifications in hybridization conditions can be empirically determined or precisely calculated based on the length and the percentage of guanosine/cytosine (GC) base pairing of the probe. The hybridization conditions can be calculated as described in Sambrook, et al., (Eds.), Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press: Cold Spring Harbor, N.Y. (1989), pp. 9.47 to 9.51
In a preferred embodiment, however, the polymerase chain reaction (PCR) is used to amplify cDNAs (or portions of full-length cDNAs) encoding a polypeptide of interest. The amplified sequences can be readily cloned into any suitable vector, e.g., expression vectors, minigene vectors, or phage display vectors. It will be appreciated that the particular method of cloning used is not critical, an long as it is possible to determine the sequence of some portion of the polypeptide of interest. As used herein, an “isolated” nucleic acid molecule or “isolated” nucleic acid sequence is a nucleic acid molecule that is either (1) identified and separated from at least one contaminant nucleic acid molecule with which it is ordinarily associated in the natural source of the nucleic acid or (2) cloned, amplified, tagged, or otherwise distinguished from background nucleic acids such that the sequence of the nucleic acid of interest can be determined, is considered isolated. An isolated nucleic acid molecule is other than in the form or setting in which it is found in nature. Isolated nucleic acid molecules therefore are distinguished from the nucleic acid molecule as it exists in natural cells. However, an isolated nucleic acid molecule includes a nucleic acid molecule contained in cells that ordinarily express the antibody where, for example, the nucleic acid molecule is in a chromosomal location different from that of natural cells.
The sequence of the amplified or cloned nucleic acid is then determined. Typically the sequence encoding the entire polypeptide is determined.
Sequencing can be carried out on clones isolated from any source, such as a single isolate, a cDNA library, or, when PCR is used, after subcloning the amplified sequence or by direct PCR sequencing of the amplified segment. Sequencing is carried out using standard techniques (see, e.g., Sambrook et al. (1989) Molecular Cloning: A Laboratory Guide, Vols 1-3, Cold Spring Harbor Press, and Sanger, F. et al. (1977) Proc. Natl. Acad. Sci. USA 74: 5463-5467, which is incorporated herein by reference).
Once isolated, the DNA may be placed into expression vectors, which are then transfected into host cells such as E. coli cells, simian COS cells, human embryonic kidney 293 cells (e.g., 293E cells), Chinese hamster ovary (CHO) cells, or myeloma cells, to obtain the synthesis of the polypeptide of interest in the recombinant host cells. Recombinant production of polypeptides is well known in the art.
Expression control sequences refers to DNA sequences necessary for the expression of an operably linked coding sequence in a particular host organism. The control sequences that are suitable for prokaryotes, for example, include a promoter, optionally an operator sequence, and a ribosome-binding site. Eukaryotic cells are known to utilize promoters, polyadenylation signals, and enhancers.
Nucleic acid is operably linked when it is placed into a functional relationship with another nucleic acid sequence. For example, DNA for a presequence or secretory leader is operably linked to DNA for a polypeptide if it is expressed as a preprotein that participates in the secretion of the polypeptide; a promoter or enhancer is operably linked to a coding sequence if it affects the transcription of the sequence; or a ribosome binding site is operably linked to a coding sequence if it is positioned so as to facilitate translation. Generally, operably linked means that the DNA sequences being linked are contiguous, and, in the case of a secretory leader, contiguous and in reading phase. However, enhancers do not have to be contiguous. Linking is accomplished by ligation at convenient restriction sites. If such sites do not exist, the synthetic oligonucleotide adaptors or linkers are used in accordance with conventional practice.
Cell, cell line, and cell culture are often used interchangeably and all such designations herein include progeny. Transformants and transformed cells, as well as transfectants and transfected cells, include the primary subject cell and cultures derived therefrom without regard for the number of transfers. It is also understood that all progeny may not be precisely identical in DNA content, due to deliberate or inadvertent mutations. Mutant progeny that have the same function or biological activity as screened for in the originally transformed cell are included. Where distinct designations are intended, it will be clear from the context.
In an alternative embodiment, the amino acid sequence of a polypeptide of interest may be determined by direct protein sequencing. Suitable encoding nucleotide sequences can be designed according to a universal codon table.
Amino acid sequence variants of the desired polypeptide may be prepared by introducing appropriate nucleotide changes into the encoding DNA, or by peptide synthesis. Such variants include, for example, deletions from, and/or insertions into and/or substitutions of, residues within the amino acid sequences of the polypeptides. Any combination of deletion, insertion, and substitution is made to arrive at the final construct, provided that the final construct possesses the desired characteristics. The amino acid changes also may alter post-translational processes of the polypeptide, such as changing the number or position of glycosylation sites.
Nucleic acid molecules encoding amino acid sequence variants of the polypeptide are prepared by a variety of methods known in the art. These methods include, but are not limited to, isolation from a natural source (in the case of naturally occurring amino acid sequence variants) or preparation by oligonucleotide-mediated (or site-directed) mutagenesis, PCR mutagenesis, and cassette mutagenesis of an earlier prepared variant or a non-variant version of the polypeptide.
The invention also provides isolated nucleic acid encoding polypeptides of the invention, optionally operably linked to control sequences recognized by a host cell, vectors and host cells comprising the nucleic acids, and recombinant techniques for the production of the polypeptides, which may comprise culturing the host cell so that the nucleic acid is expressed and, optionally, recovering the polypeptide from the host cell culture or culture medium.
For recombinant production of the polypeptide, the nucleic acid encoding the polypeptide is isolated and inserted into a replicable vector for further cloning (amplification of the DNA) or for expression. DNA encoding the polypeptide is readily isolated and sequenced using conventional procedures (e.g., by using oligonucleotide probes that are capable of binding specifically to genes encoding the polypeptide). Many vectors are available. The vector components generally include, but are not limited to, one or more of the following: a signal sequence, an origin of replication, one or more selective marker genes, an enhancer element, a promoter, and a transcription termination sequence.
(1) Signal sequence component: The polypeptides of this invention may be produced recombinantly not only directly, but also as a fusion polypeptide with a heterologous polypeptide, which is preferably a signal sequence or other polypeptide having a specific cleavage site at the N-terminus of the mature protein or polypeptide. The signal sequence selected preferably is one that is recognized and processed (i.e., cleaved by a signal peptidase) by the host cell. If prokaryotic host cells do not recognize and process the native polypeptide signal sequence, the signal sequence may be substituted by a signal sequence selected, for example, from the group of the pectate lyase (e.g., pelB) alkaline phosphatase, penicillinase, 1 pp, or heat-stable enterotoxin II leaders. For yeast secretion the native signal sequence may be substituted by, e.g., the yeast invertase leader, a factor leader (including Saccharomyces and Kluyveromyces α-factor leaders), or acid phosphatase leader, the C. albicans glucoamylase leader, or the signal described in WO90/13646. In mammalian cell expression, mammalian signal sequences as well as viral secretory leaders, for example, the herpes simplex gD signal, are available.
The DNA for such precursor region is ligated in reading frame to DNA encoding the polypeptide.
(2) Origin of replication component: Each of expression and cloning vectors contain a nucleic acid sequence that enables the vector to replicate in one or more selected host cells. Generally, in cloning vectors this sequence is one that enables the vector to replicate independently of the host chromosomal DNA, and includes origins of replication or autonomously replicating sequences. Such sequences are well known for a variety of bacteria, yeast, and viruses. The origin of replication from the plasmid pBR322 is suitable for most Gram-negative bacteria, the 2 μm plasmid origin is suitable for yeast, and various viral origins are useful for cloning vectors in mammalian cells. Generally, the origin of replication component is not needed for mammalian expression vectors (the SV40 origin may typically be used only because it contains the early promoter).
(3) Selective marker component: Expression and cloning vectors may contain a selective gene, also termed a selectable marker. Typical selection genes encode proteins that (a) confer resistance to antibiotics or other toxins, e.g., ampicillin, neomycin, methotrexate, tetracycline, G418, geneticin, histidinol, or mycophenolic acid (b) complement auxotrophic deficiencies, or (c) supply critical nutrients not available from complex media, e.g., the gene encoding D-alanine racemase from Bacillus.
One example of a selection scheme utilizes a drug to arrest growth of a host cell. Those cells that are successfully transformed with a heterologous gene produce a protein conferring drug resistance and thus survive the selection regimen. Examples of such dominant selection use the drugs methotrexate, neomycin, histidinol, puromycin, mycophenolic acid and hygromycin.
Another example of suitable selectable markers for mammalian cells are those that enable the identification of cells competent to take up the polypeptide-encoding nucleic acid, such as DHFR, thymidine kinase, metallothionein-I and -II, preferably primate metallothionein genes, adenosine deaminase, ornithine decarboxylase, etc.
For example, cells transformed with the DHFR selection gene are first identified by culturing all of the transformants in a culture medium that contains methotrexate (Mtx), a competitive antagonist of DHFR. An appropriate host cell when wild-type DHFR is employed is the Chinese hamster ovary (CHO) cell line deficient in DHFR activity.
Alternatively, host cells (particularly wild-type hosts that contain endogenous DHFR) transformed or co-transformed with DNA sequences encoding the polypeptide of the invention, wild-type DHFR protein, and another selectable marker such as aminoglycoside 3′-phosphotransferase (APH) can be selected by cell growth in medium containing a selection agent for the selectable marker such as an aminoglycoside antibiotic, e.g., kanamycin, neomycin, or G418. See U.S. Pat. No. 4,965,199.
A suitable selection gene for use in yeast is the trp1 gene present in the yeast plasmid YRp7 (Stinchcomb et al., Nature, 282: 39 (1979)). The trp1 gene provides a selection marker for a mutant strain of yeast lacking the ability to grow in tryptophan, for example, ATCC No. 44076 or PEP4-1. Jones, (Genetics 85:12 (1977)). The presence of the trp1 lesion in the yeast host cell genome then provides an effective environment for detecting transformation by growth in the absence of tryptophan. Similarly, Leu2-deficient yeast strains (ATCC 20,622 or 38,626) are complemented by known plasmids bearing the Leu2 gene. Ura3-deficient yeast strains are complemented by plasmids bearing the ura3 gene.
In addition, vectors derived from the 1.6 μm circular plasmid pKD1 can be used for transformation of Kluyveromyces yeasts. Alternatively, an expression system for large-scale production of recombinant calf chymosin was reported for K. lactis Van den Berg, (Bio/Technology, 8:135 (1990)). Stable multi-copy expression vectors for secretion of mature recombinant human serum albumin by industrial strains of Kluyveromyces have also been disclosed (Fleer et al, Bio/Technology, 9:968-975 (1991)).
(4) Promoter component: Expression and cloning vectors usually contain a promoter that is recognized by the host organism and is operably linked to the polypeptide-encoding nucleic acid. Promoters suitable for use with prokaryotic hosts include the arabinose (e.g., araB) promoter phoA promoter, β-lactamase and lactose promoter systems, alkaline phosphatase, a tryptophan (trp) promoter system, and hybrid promoters such as the tac promoter. However, other known bacterial promoters are suitable. Promoters for use in bacterial systems also will contain a Shine-Dalgarno (S.D.) sequence operably linked to the DNA encoding the polypeptide of the invention.
Promoter sequences are known for eukaryotes. Virtually all eukaryotic genes have an AT-rich region located approximately 25 to 30 bases upstream from the site where transcription is initiated. Another sequence found 70 to 80 bases upstream from the start of transcription of many genes is a CNCAAT region where N may be any nucleotide. At the 3′ end of most eukaryotic genes is an AATAAA sequence that may be the signal for addition of the poly A tail to the 3′ end of the coding sequence. All of these sequences are suitably inserted into eukaryotic expression vectors.
Examples of suitable promoting sequences for use with yeast hosts include the promoters for 3-phosphoglycerate kinase or other glycolytic enzymes, such as enolase, glyceraldehyde-3-phosphate dehydrogenase, hexokinase, pyruvate decarboxylase, phosphofructokinase, glucose-6-phosphate isomerase, 3-phosphoglycerate mutase, pyruvate kinase, triosephosphate isomerase, phosphoglucose isomerase, and glucokinase.
Other yeast promoters, which are inducible promoters having the additional advantage of transcription controlled by growth conditions, are the promoter regions for alcohol dehydrogenase 2, isocytochrome C, acid phosphatase, degradative enzymes associated with nitrogen metabolism, metallothionein, glyceraldehyde-3-phosphate dehydrogenase, and enzymes responsible for maltose and galactose utilization. Suitable vectors and promoters for use in yeast expression are further described in EP 73,657. Yeast enhancers also are advantageously used with yeast promoters.
Polypeptide transcription from vectors in mammalian host cells is controlled, for example, by promoters obtained from the genomes of viruses such as Abelson leukemia virus, polyoma virus, fowlpox virus, adenovirus (such as Adenovirus 2), bovine papilloma virus, avian sarcoma virus, most preferably cytomegalovirus, a retrovirus, hepatitis-B virus, Simian Virus 40 (SV40), from heterologous mammalian promoters, e.g., the actin promoter or an immunoglobulin promoter, from heat-shock promoters, provided such promoters are compatible with the host cell systems.
The early and late promoters of the SV40 virus are conveniently obtained as an SV40 restriction fragment that also contains the SV40 viral origin of replication. The immediate early promoter of the human cytomegalovirus is conveniently obtained as a HindIII E restriction fragment. A system for expressing DNA in mammalian hosts using the bovine papilloma virus as a vector is disclosed in U.S. Pat. No. 4,419,446. A modification of this system is described in U.S. Pat. No. 4,601,978. See also Reyes et al., Nature 297: 598-601 (1982) on expression of human β-interferon cDNA in mouse cells under the control of a thymidine kinase promoter from herpes simplex virus. Alternatively, the Rous sarcoma virus long terminal repeat can be used as the promoter.
(5) Enhancer element component: Transcription of a DNA encoding the polypeptide of this invention by higher eukaryotes is often increased by inserting an enhancer sequence into the vector. Many enhancer sequences are known from mammalian genes (globin, elastase, albumin, alpha-fetoprotein, and insulin). Typically, however, one will use an enhancer from a eukaryotic cell virus. Examples include the SV40 enhancer on the late side of the replication origin (bp 100-270), the cytomegalovirus early promoter enhancer, the polyoma enhancer on the late side of the replication origin, and adenovirus enhancers. See also Yaniv, Nature 297:17-18 (1982) on enhancing elements for activation of eukaryotic promoters. The enhancer may be spliced into the vector at a position 5′ or 3′ to the antibody-encoding sequence, but is preferably located at a site 5′ from the promoter.
(6) Transcription termination component: Expression vectors used in eukaryotic host cells (yeast, fungi, insect, plant, animal, human, or nucleated cells from other multicellular organisms) will also contain sequences necessary for the termination of transcription and for stabilizing the mRNA. Such sequences are commonly available from the 5′ and, occasionally 3′, untranslated regions of eukaryotic or viral DNAs or cDNAs. These regions contain nucleotide segments transcribed as polyadenylated fragments in the untranslated portion of the mRNA encoding antibody. One useful transcription termination component is the bovine growth hormone polyadenylation region. See WO94/11026 and the expression vector disclosed therein. Another is the mouse immunoglobulin light chain transcription terminator.
(7) Selection and transformation of host cells: Suitable host cells for cloning or expressing the DNA in the vectors herein are the prokaryote, yeast, or higher eukaryote cells described above. Suitable prokaryotes for this purpose include eubacteria, such as Gram-negative or Gram-positive organisms, for example, Enterobacteriaceae such as Escherichia, e.g., E. coli, Enterobacter, Erwinia, Klebsiella, Proteus, Salmonella, e.g., Salmonella typhinwrium, Serratia, e.g., Serratia marcescans, and Shigella, as well as Bacilli such as B. subtilis and B. licheniformis (e.g., B. licheniformis 41 P disclosed in DD 266,710 published Apr. 12, 1989), Pseudomonas such as P. aeruginosa, and Streptomyces. One preferred E. coli cloning host is E. coli 294 (ATCC 31,446), although other strains such as E. coli B, E. coli X1776 (ATCC 31,537), and E. coli W3110 (ATCC 27,325) are suitable. These examples are illustrative rather than limiting.
In addition to prokaryotes, eukaryotic microbes such as filamentous fungi or yeast are suitable cloning or expression hosts for antibody-encoding vectors. Saccharomyces cerevisiae, or common baker's yeast, is the most commonly used among lower eukaryotic host microorganisms. However, a number of other genera, species, and strains are commonly available and useful herein, such as Schizosaccharomyces pombe; Kluyveromyces hosts such as, e.g., K. lactis, K. fragilis (ATCC 12,424), K. bulgaricus (ATCC 16,045), K. wickeramii (ATCC 24,178), K. waltii (ATCC 56,500), K. drosophilarum (ATCC 36,906), K. thermotolerans, and K. Inctrxianus; yarrowia (EP 402,226); Pichia pastoris (EP 183,070); Candida; Trichoderma reesia (EP 244,234); Neurospora crassa; Schwanniomyces such as Schwanniomyces occidentalis; and filamentous fungi such as, e.g., Neurospora, Penicillium, Tolypocladium, and Aspergillus hosts such as A. nidulans and A. niger.
Suitable host cells for the expression of polypeptides are derived from multicellular organisms. Examples of invertebrate cells include plant and insect cells. Numerous baculoviral strains and variants and corresponding permissive insect host cells from hosts such as Spodoptera frugiperda (caterpillar), Aedes aegypti (mosquito), Aedes albopictus (mosquito), Drosophila melanogaster (fruitfly), and Bombyx mori have been identified. A variety of viral strains for transfection are publicly available, e.g., the L-1 variant of Autographa californica NPV and the Bm-5 strain of Bombyx mori NPV, and such viruses may be used as the virus herein according to the present invention, particularly for transfection of Spodoptera frugiperda cells.
Plant cell cultures of cotton, corn, potato, soybean, petunia, tomato, tobacco, lemna, and other plant cells can also be utilized as hosts.
Examples of useful mammalian host cell lines are Chinese hamster ovary cells, including CHOK1 cells (ATCC CCL61), DXB-11, DG-44, and Chinese hamster ovary cells/-DHFR (CHO, Urlaub et al., Proc. Natl. Acad. Sci. USA 77: 4216 (1980)); monkey kidney CV1 line transformed by SV40 (COS-7, ATCC CRL 1651); human embryonic kidney line (293 or 293 cells subcloned for growth in suspension culture, (Graham et al., J. Gen Virol. 36: 59, 1977); baby hamster kidney cells (BHK, ATCC CCL 10); mouse sertoli cells (TM4, Mather, (Biol. Reprod. 23: 243-251, 1980); monkey kidney cells (CV1 ATCC CCL 70); African green monkey kidney cells (VERO-76, ATCC CRL-1587); human cervical carcinoma cells (HELA, ATCC CCL 2); canine kidney cells (MDCK, ATCC CCL 34); buffalo rat liver cells (BRL 3A, ATCC CRL 1442); human lung cells (W138, ATCC CCL 75); human liver cells (Hep G2, HB 8065); mouse mammary tumor (MMT 060562, ATCC CCL51); TRI cells (Mather et al., Annals N.Y Acad. Sci. 383: 44-68 (1982)); MRC 5 cells; FS4 cells; and a human hepatoma line (Hep G2).
Host cells are transformed or transfected with the above-described expression or cloning vectors for polypeptide production and cultured in conventional nutrient media modified as appropriate for inducing promoters, selecting transformants, or amplifying the genes encoding the desired sequences. In addition, novel vectors and transfected cell lines with multiple copies of transcription units separated by a selective marker are particularly useful and preferred for the expression of polypeptides.
(8) Culturing the host cells: The host cells used to produce the polypeptides of this invention may be cultured in media suitable for promoting growth in the cell expression system utilized. Yeast and baceterial cells may be expressed using media well-known in the art, such as defined media, undefined media or dropout media (e.g., lacking certain amino acids or sugars for selection of cells) as appropriate for the expression system used. Commercially available media such as Ham's F10 (Sigma), Minimal Essential Medium ((MEM), (Sigma), RPMI-1640 (Sigma), and Dulbecco's Modified Eagle's Medium ((DMEM), Sigma) are suitable for culturing mammalian host cells. In addition, any of the media described in Ham et al., (Meth. Enz. 58: 44, 1979), Barnes et al., Anal. Biochem. 102: 255 (1980), U.S. Pat. Nos. 4,767,704; 4,657,866; 4,927,762; 4,560,655; or 5,122,469; WO90103430; WO 87/00195; or U.S. Pat. Re. No. 30,985 may be used as culture media for the host cells. Any of these media may be supplemented as necessary with hormones and/or other growth factors (such as insulin, transferrin, or epidermal growth factor), salts (such as sodium chloride, calcium, magnesium, and phosphate), buffers (such as HEPES), nucleotides (such as adenosine and thymidine), antibiotics (such as GENTAMYCIN™ drug), trace elements (defined as inorganic compounds usually present at final concentrations in the micromolar range), and glucose or an equivalent energy source. Any other necessary supplements may also be included at appropriate concentrations that would be known to those skilled in the art. The culture conditions, such as temperature, pH, and the like, are those previously used with the host cell selected for expression, and will be apparent to the ordinarily skilled artisan.
(9) Purification of polypeptides: When using recombinant techniques, the polypeptide can be produced intracellularly, in the periplasmic space, or directly secreted into the medium, including from microbial cultures. If the polypeptide is produced intracellularly, as a first step, the particulate debris, either host cells or lysed fragments, is removed, for example, by centrifugation or ultrafiltration. Better et al. (Science 240:1041-43, 1988; ICSU Short Reports 10:105 (1990); and Proc. Natl. Acad. Sci. USA 90:457-461 (1993) describe a procedure for isolating antibodies which are secreted to the periplasmic space of E. coli. [See also, (Carter et al., Bio/Technology 10:163-167 (1992)].
The polypeptide composition prepared from microbial or mammalian cells can be purified using, for example, hydroxylapatite chromatography cation or anion exchange chromatography, and affinity chromatography, with affinity chromatography being a preferred purification technique. Mechanically stable matrices such as controlled pore glass or poly(styrenedivinyl)benzene allow for faster flow rates and shorter processing times than can be achieved with agarose. Other techniques for protein purification such as fractionation on an ion-exchange column, ethanol precipitation, Reverse Phase HPLC, chromatography on silica, chromatography on heparin SEPHAROSE® chromatography on an anion or cation exchange resin (such as a polyaspartic acid column), chromatofocusing, SDS-PAGE, ammonium sulfate precipitation and immunoaffinity are also available depending on the polypeptide to be recovered.
Antibodies
In one embodiment, the invention contemplates an antibody that is specifically reactive with the polypeptides described herein. As used herein “antibody” refers to an antibody or fragment thereof, or a polypeptide comprising an antigen binding domain of an antibody. Exemplary antibodies or antibody fragments include polyclonal antibodies, monoclonal antibodies, chimeric antibodies, humanized antibodies, human antibodies, multispecific antibodies, Fab, Fab′, F(ab′)2, Fv, domain antibody (dAb), complementarity determining region (CDR) fragments, CDR-grafted antibodies, single-chain antibodies (scFv), single chain antibody fragments, chimeric antibodies, diabodies, triabodies, tetrabodies, minibody, linear antibody; chelating recombinant antibody, a tribody or bibody, an intrabody, a nanobody, a small modular immunopharmaceutical (SMIP), a antigen-binding-domain immunoglobulin fusion protein, a camelized antibody, a VHH containing antibody, or a variant or a derivative thereof, and polypeptides that contain at least a portion of an immunoglobulin that is sufficient to confer specific antigen binding to the polypeptide, such as one, two, three, four, five or six CDR sequences.
As used herein, an antibody that “specifically binds” is “antigen specific,” is “specific for” antigen target or is “immunoreactive” with an antigen refers to an antibody that binds an antigen with greater affinity than other antigens of similar sequence. In one aspect, the antibodies contemplated, or fragments, variants, or derivatives thereof, will bind with a greater affinity to target antigen as compared to its binding affinity to similar antigens derived form other sources, e.g., other species, but antibodies that recognize and bind orthologs of the target are within the scope of the invention.
Immunoglobulins can be assigned to different classes, IgA, IgD, IgE, IgG and IgM, which may be further divided into subclasses or isotypes, e.g. IgG1, IgG2, IgG3, IgG4, IgA1 and IgA2. The subunit structures and three-dimensional configurations of different classes of immunoglobulins are well known. An antibody contemplated herein, if it comprises a constant domain, may be of any of these subclasses or isotypes.
Various procedures known in the art may be used for the production of polyclonal or monoclonal antibodies to the polypeptide of the invention. For the production of antibodies, various host animals (including but not limited to rabbits, mice, rats, hamsters, and the like) are immunized by injection with a polypeptide described herein. Various adjuvants may be used to increase the immunological response, depending on the host species, including but not limited to Freund's (complete and incomplete) adjuvant, mineral gels such as aluminum hydroxide, surface active substances such as lysolecithin, pluronic polyols, polyanions, oil emulsions, keyhole limpet hemocyanins, dinitrophenol, and potentially useful human adjuvants such as BCG (Bacille Calmette-Guerin) and Corynebacterium parvum.
Monoclonal antibodies may be made by techniques well-known in the art, including, but not limited to the hybridoma technique originally described by Köhler et al., Nature, 256: 495-497 (1975), and the more recent human B-cell hybridoma technique [Kosbor et al., Immunology Today, 4:72 (1983)] and the EBV-hybridoma technique [Cole et al., Monoclonal Antibodies and Cancer Therapy, Alan R Liss, Inc., pp. 77-96 (1985),] or by recombinant DNA methods (see, e.g., U.S. Pat. No. 4,816,567) (all specifically incorporated herein by reference). The monoclonal antibodies may also be isolated from phage antibody libraries using the techniques described in, for example, Clackson et al., (Nature 352:624-628, 1991) and Marks et al., (J. Mol. Biol. 222:581-597, 1991).
In addition to the production of monoclonal antibodies, techniques developed for the production of “chimeric antibodies,” e.g., the splicing of an antibody gene from one species to antibody genes of another species to obtain a molecule with appropriate antigen specificity and biological activity, can be used [Morrison et al., Proc. Natl. Acad. Sci. 81:6851-6855 (1984); Neuberger et al., Nature 312:604-608 (1984); Takeda et al., Nature 314:452-454 (1985)]. Alternatively, techniques described for the production of single-chain antibodies (U.S. Pat. No. 4,946,778) can be adapted to produce antibodies.
Antibody fragments that contain the idiotype of the molecule may be generated by known techniques. For example, such fragments include, but are not limited to, the F(ab′)2 fragment which may be produced by pepsin digestion; the Fab′ fragments which may be generated by reducing the disulfide bridges of the F(ab′)2 fragment, and the two Fab fragments which may be generated by treating the antibody molecule with papain and a reducing agent. Additionally, using techniques known in the art to isolate CDRs, compositions comprising CDRs are generated. CDRs are characterized by six polypeptide loops, three loops for each of the heavy or light chain variable regions. The amino acid position in a CDR is defined by Kabat et al., “Sequences of Proteins of Immunological Interest,” U.S. Department of Health and Human Services (1983), which is incorporated herein by reference.
Screening assays to determine binding specificity of an antibody for use in the methods of the invention are well known and routinely practiced in the art. For a comprehensive discussion of such assays, see Harlow et al. (Eds), Antibodies A Laboratory Manual; Cold Spring Harbor Laboratory; Cold Spring Harbor, N.Y. (1988), Chapter 6. Antibodies for use in the invention can be produced using any method known in the art.
The following examples are provided to illustrate the invention, but are not intended to limit the scope thereof.
Chemical Synthesis
##STR00005## ##STR00006##
##STR00007##
(Anzalone, et al. J. Org. Chem. 70(6):2091-2096 (2005) and Spafford et al., Tetrahedron Lett. 48(49):8665-8667 (2007)). An oven-dried flask was charged with a solution of 4 (2.023 g, 1.0 equiv) in CH2Cl2 (50 mL). To this solution was added BiBr3 (449 mg, 10 mol %), and the resulting suspension was treated with allyltrimethylsilane (1.71 g, 1.5 equiv). The reaction mixture was stirred for 4 h at rt, and quenched by pouring into a separatory funnel containing 1 M HCl (50 mL). The organic layer was washed with saturated NaHCO3 (50 mL) and brine (50 mL), dried (Na2SO4, and the solvent was removed in vacuo. The crude residue was purified by chromatography on SiO2 (2% EtOAc/hexanes) to afforded 2(1.508 g, 71%) as a colorless oil: 1H NMR (CDCl3) 5.9-5.75 (m, 1H), 5.1-5.0 (m, 2H). 3.35; (s, 3H), 3.21 (p, 1H, J=5.7 Hz), 2.29-2.25 (m, 2H), 1.50-1.40 (m, 2H), 1.40-1.25 (m, 14H), 0.90 (t, 3H, J=6.9 Hz); 13C NMR (CDCl3)
134.9, 116.6, 80.4, 56.4, 37.7, 33.3, 31.8, 29.7, 29.5, 29.3, 25.2, 22.6, 14.0.
##STR00008##
A solution of 3 (424.7 mg. 1.0 equiv) in THF (8 mL) was treated with NaIO4 (2.14 g, 5.0 equiv) and water (4 mL). The reaction mixture was stirred at rt for ca. 2 min, treated with OsO4 (0.67 mL of a 0.3 M solution in toluene) and stirred at rt for 3 h. The mixture was poured into a separatory funnel containing H2O (10 mL) and EtOAc (10 mL). The organic layer was washed with brine (20 mL), dried (Na2SO4), and the solvent was removed in vacuo to afford a pale yellow oil. Purification by chromatography on SiO2 (2% EtOAc/hexanes to 4% EtOAc/hexanes) afforded 5 (253 mg, 59%) as a pale yellow oil that was used without further purification: 1H NMR (CDCl3) 9.8 (t, 1H, J=1 Hz), 3.75-3.65 (m, 1H), 3.34 (s, 3H), 2.65-2.45 (m, 2H), 1.70-1.40 (m, 2H), 1.40-1.20 (m, 14H), 0.85 (t, 3H, J=6.8 Hz).
##STR00009##
A solution of N,N′-(1R,1′R)-1,1′-(benzylazanediyl)bis(2-methylpropane-1,1-diyl)bis(1,1,1-trifluoromethanesulfonamide) (81.2 mg, 0.15 mmol, 30 mol %) in CH2Cl2 (1 mL) was treated at rt under N2 slowly with a solution of AlMe3 (10.8 mg, 0.15 mmol) in CH2Cl2 (0.5 mL). The mixture was stirred at room temperature (rt) for 2 h, cooled to −45° C. and treated sequentially with diisopropylethylamine (11 mg, 1.7 equiv), acetyl bromide (117 mg, 1.9 equiv) and 5 (107 mg, 0.500 mmol, 1.0 equiv). The resulting pale yellow solution was stirred for 14 h at −45° C., warmed to rt, and poured into a separatory funnel containing 0.1 N HCl (10) mL). The organic layer was washed with saturated NaHCO3, brine, and dried (Na2SO4). The solvent was removed in vacuo and the yellow oily product was purified by chromatography on SiO2 (4% EtOAc/hexanes to 6% EtOAc/hexanes) to give 6 (99.1 mg, 77%) as a colorless oil: 1H NMR (CDCl3) 4.8-4.65 (m, 1H), 3.60-3.50 (m, 1H), 3.3-3.2 (m, 1H), 3.35, 3.32 (2s, 3H), 3.22-3.08 (m, 1H), 2.18-1.82 (m, 2H) 1.65-1.35 (m, 2H), 1.35-1.20 (m, 14H), 0.90-0.80 (m, 3H).
##STR00010##
(ref. Gu, et al. Nature 459, 731-735 (2009)). To a solution of 6 (92.0 mg, 0.359 mmol, 1.0 equiv) in THF (1.5 mL) was added a solution of NaOH (15.7 mg, 0.394 mmol, 1.1 equiv) in water (1.5 mL). The reaction mixture was stirred at rt for 1 h. During this time, its appearance changed from turbid to clear (t=about 0.5 h). The solution was quenched by addition of 1 M HCl (1 mL) and extracted with ether (2×5 mL). The combined organic layers were washed with water (5 mL) and brine (5 mL), dried (Na2SO4) and concentrated in vacuo to afford a pale yellow oil. Purification of the crude product by chromatography on SiO2 (1:1 EtOAc/hexanes containing 0.5% AcOH) provided (3R)-1 (94.4 mg, 96%) as a colorless oil: ATR/IR 2920, 2851, 1709, 1413, 1187, 1079, 736 cm−1; 1H NMR (CDCl3) 4.35-4.20 (m, 1H), 3.55-3.45 (m, 1H), 3.38, 3.37 (2s, 3H), 2.56-2.50 (m, 2H), 1.80-1.35 (m, 3H), 1.35-1.25 (m, 14H), 0.90 (t, 3H, J=6.9 Hz); 13C NMR (CDCl3)
176.4, 175.7, 68.1, 65.4, 56.7, 56.0, 41.6, 41.5, 39.7, 39.1, 32.9, 32.8, 31.9, 29.8, 29.6, 29.5, 29.3, 25.2, 24.5, 22.7, 14.1.
##STR00011##
(ref. Nelson, et al., J. Am. Chem. Soc. 121(41):9742-9743 (1999)). A solution of N,N′-(1S,1′S)-1,1′-(benzylazanediyl)bis(2-methylpropane-1,1-diyl)bis(1,1,1-trifluoromethanesulfonamide) (81.2 mg, 0.15 mmol, 30 mol %) in CH2Cl2 (1 mL) was treated at rt under N2 slowly with a solution of AlMe3 (10.8 mg, 0.15 mmol) in CH2Cl2 (0.5 mL). The mixture was stirred at rt for 2 h, cooled to −45° C. and treated sequentially with diisopropylethylamine (11 mg, 1.7 equiv), acetyl bromide (117 mg, 1.9 equiv) and 3 (107 mg, 0.500 mmol, 1.0 equiv). The resulting pale yellow solution was stirred for 14 h at −45° C., warmed to rt, and poured into a separatory funnel containing 0.1 N HCl (10 mL). The organic layer was washed with saturated NaHCO3, brine, and dried (Na2SO4). The solvent was removed in vacuo and the yellow oily product was purified by chromatography on SiO2 (4% EtOAc/hexanes to 6% EtOAc/hexanes) to give 7 (87 mg, 81%) as a colorless oil that was saponified without further purification.
##STR00012##
To a solution of 7 (187 mg, 0.729 mmol, 1.0 equiv) in THF (2.5 mL) was added a solution of NaOH (32.) mg, 0.802 mmol, 1.1 equiv) in water (1 L). The reaction mixture was stirred at rt for 2 h, transferred to a separatory funnel, diluted with water (5 mL) and extracted with ether. The aqueous layer was acidified with 2 N HCl (3 mL) and extracted with ether (2×15 mL). The combined organic layers were dried (Na2SO4) and concentrated in vacuo to afford (3S)-1 (187 mg, 93%) as a colorless oil that was used without further purification: ATR/IR 2920, 2851, 1709, 1412, 1189, 1079, 738 cm−1; 1H NMR (CDCl3) 4.85-4.7 (m, 1H), 3.55-3.45 (m, 1H), 3.39, 3.38 (2s, 3H), 2.56-2.52 (m, 2H), 1.80-1.35 (m, 3H), 1.35-1.25 (m, 14H), 0.90 (t, 3H, J=6.9 Hz); 13C NMR (CDCl3)
176.5, 175.8, 81.5, 78.7, 68.0, 65.3, 56.7, 55.9, 41.5, 39.6, 39.0, 32.8, 32.6, 31.8, 29.7, 29.5, 29.2, 25.1, 24.4, 22.6, 14.1; MS (EI) m/z 274 (M+, 0.5), 256 (0.5), 171, 25, 129 (100), 97 (15).
##STR00013##
(ref. Strehmel, et al., Tetrahedron Letters 49(4):586-588 (2008)). To a solution of 5 (5.5 mg, 0.02 mmol, 1.0 equiv) in methylene chloride (1 mL) was added slowly a solution of trimethylsilyl chlorosulfonate (3.8 mg, 0.02 mmol, 1.0 equiv) in methylene chloride (1 mL) under N2. The reaction mixture was stirred at 0° C. for 6 h before warmed it up to rt. The mixture was concentrated in vacuo to yield a pale yellow oil containing (3R)-2 (about 65% yield), which was applied as an authentic standard for the intermediates of ST and TE reactions. Due to instability of (3R)-2, the mixture was not purified before subjected to LC-MS and MS/MS analysis. MS (ESI) calculated for [M-H]− 353.17, found 353.09. MS/MS fragmentation of 353.09, found 273.17 and 309.09, corresponding to the losses of SO3 and CO2 respectively.
(3R)-1-CoA/(3S)-1-CoA.
The CoA thioesterification of (3R)-1 and (3S)-1, as we as product purification, was performed in the similar way as previously described Gu, et al., J. Am. Chem. Soc. 128(28):9014-9015 (2006) and Geders, et al., J. Biol. Chem., 282:35954-35963(2007)). For both (3R)-1-CoA and (3S)-1-CoA, MS (ESI) calculated for [M-H]− 1022.32, found 1022.28.
Bioinformatic Analysis for Prediction of CurM KR Stereospecificity
Based on alignments of KR domains, the CurL and CurM KR domains contain the LDD motif, indicating that they catalyze formation B-type hydroxyl groups. Chirality of the carbon atom bearing the methoxyl group in curacin A confirms the prediction for CurL KR stereospecificity.
Bacterial Strains, Media and Culture Conditions
Escherichia coli DH5α MCR (Invitrogen) was used for DNA propagation. E. coli BL21 (DE3) transformed with the pET24b and pET28b constructs were used for protein overexpression in Luria-Bertani medium. Ampicillin (100 μg/mL), carbenicillin (100 μg/mL), kanamycin (50 μg/mL), and apramycin (50 μg/mL) were used for the corresponding plasmid construct resistance marker selection in E. coli cultures.
DNA Sequencing of curM and 3′ Flanking Region
To identify cosmids containing the 3′ end of cur gene cluster, the previous cosmid genomic library of L. majuscula strain L19 (Chang et al, Gene 296, 235-247 (2002)) was screened by PCR using an oligonucleotide primer pair to amplify the curM ST gene: (F) 5′-GGA TGC GGA TGC AAA AAC TTG-3′ (SEQ ID NO: 6) and (R) 5′-CGG ATG CAA AAA CTT GTC GGG-3′ (SEQ ID NO: 7). Two cosmids, pLM14 and pLM19, in addition to pLM17, were identified to contain curM ST. These three cosmids were also examined by comparing their restriction enzyme digestion patterns. The pLM14 was chosen to be sequenced by primer walking method for the 3′ end of curM and the flanking region. The new sequence was compared with the genome sequencing data (unpublished), and is SEQ ID NO: 1 (amino acid sequence) and SEQ ID NO: 2 (DNA sequence).
Plasmid Construction
CurM ACP, ST and TE genes were amplified from the pLM14. The CurM ACP and TE genes were inserted into pET24b plasmid at the NdeI and NotI restriction sites. The CurM ST gene was inserted into pET28b plasmid with NdeI and BamHI restriction sites. All the constructs were verified by DNA sequencing. The primers for the plasmid construction are: ACP (F): 5′-CAT ATG ACA GAC GAA CGC ATT TTA G-3′(SEQ ID NO: 8), ACP (R): 5′-GCG GCC GCT AAG CTT GTT GGA GAT GG-3′(SEQ ID NO: 9), ST (F): 5′-CAT ATG ATC TTT GCA ACC AAA AGT TCA-3′(SEQ ID NO: 10), ST (R): 5′-GGA TCC TTA TTG AGG CTG TTG ATT TGT CG-3′(SEQ ID NO: 16), TE (F): 5′-CAT ATG CAA GTC TCT ACA ACT CCC T-3′(SEQ ID NO: 17), and TE (R): 5′-GCG GCC GCG GAT GTT AAG ATA AGT GAT GC-3′(SEQ ID NO: 18).
Protein Overexpression
E. coli BL21 (DE3) was transformed with pET24b::ACP or pET24b::TE plasmid to overexpress C-terminal His-tagged proteins, and by pET28b::ST plasmid to overexpress N-terminal His-tagged protein. ACP was overexpressed in the apo form. Cells were grown at 30° C. to an OD (590 nm)=0.5-0.6, and then cooled to 15° C. prior to the addition of 1 mM isopropyl-β-D-galactopyranoside. The cultures were grown at 15° C. for another 18-20 h before harvesting.
Protein Purification
Protein purifications were performed at 4° C. E. coli cells were harvested by centrifugation (5,000 g, 15 min, 4° C.), resuspended in ice cold lysis buffer A (50 mM PBS buffer, pH 8.0, 300 mM NaCl, 10 mM imidazole, 20% glycerol) and disrupted by sonication on ice. The cell debris was removed by centrifugation at 15,000 g for 50 min. The supernatant was gently removed and loaded onto the 5 ml HisTrap column (GE Healthcare pre-equilibrated with lysis buffer A. The resin was washed successively with ˜10 column volumes of the washing buffer B (50 mM PBS buffer, pH 8.0, 300 mM NaCl, 20 mM imidazole, 10% glycerol) to remove nonspecifically bound contaminants. Bound proteins were eluted with imidazole by a linear gradient of the elution buffer C (50 mM PBS buffer, pH 8.0, 300 mM NaCl, 250 mM imidazole, 20% glycerol). The eluate fractions were examined by SDS-PAGE for purity, pooled and concentrated using Amicon Ultra-15 (10 kDa or 5 kDa) centrifugal devices (Millipore). The concentrated eluate was loaded onto HiLoad 26/60 Superdex 200 column (GE Healthcare) equilibrated with the storage buffer D (50 mM PBS buffer, pH 7.5, 200 mM NaCl, 20% glycerol). The fractions were pooled, concentrated, flash-frozen in 50-100 μl aliquots in liquid N2, and stored at −80° C. for future use. The purity of the proteins was analyzed by SDS-PAGE and the protein concentrations were determined using the Bradford assay (Bio-Rad).
Preparation of the ACP-Linked Substrates
The (3R)-1-ACP and (3S)-1-ACP substrates were prepared by loading the (3R)-1-CoA and (3S)-1-CoA onto the (apo) CurM ACP by using S. verticillus Svp. Briefly, 500 μM acyl-CoA and 50 μM (apo) ACP were incubated with 10 μM Svp, and 10 mM MgCl2 in 50 mM Tris-HCl buffer, pH 8.1, at room temperature for about 2 h. Reaction mixtures were desalted by PD10 column equilibrated with buffer D. The desalted acyl-ACPs were concentrated by using Amicon Ultra-4 (5 kDa, Millipore), flash-frozen in 10-50 μl aliquots in liquid N2, and stored at −80° C. The ACP samples were analyzed by reverse-phase HPLC using a Jupiter C4 column (250×2.0 mm, 5 μm, 300 Å, Phenomenex), and a linear elution gradient from 5% to 100% of CH3CN (0.1% CF3CO2H)/H2O (0.1% CF3CO2H).
Kinetic Studies of TE Hydrolysis Using CoA-Linked Substrates
HPLC-based analyses of the TE hydrolysis were performed using XBridge C18 column (4.6×250 mm, 5 μm, Waters) on the Gold HPLC system equipped with an autosampler and controlled by 32 Karat software (Beckman Coulter). Samples were eluted with a linear gradient from 10% to 90% of MeOH/H2O (10 mM CH3CO2NH4). For steady state kinetic studies. TE hydrolysis was examined in 40 μl 50 mM Tris-HCl buffer (pH 7.0) with 100 μM, 200 μM, 500 μM, 1000 μM and 2000 μM (3R)-1-CoA or (3S)-1-CoA. 1.25 μM TE was incubated with the CoA substrates at room temperature for 10 min before quenched by 40 μl 1M CH3CO2H. The reaction mixtures were then added with isovaleryl-CoA as an internal standard before filtered by Microcon YM-10 (Millipore), neutralized by 20 μl 1M NaOH, and stored at −80° C. before HPLC analysis. Control reactions without enzymes were run at the same time. The TE hydrolysis reaction was measured by consumption of CoA substrates. The HPLC peak areas of CoA substrates were normalized based on the internal standards.
ST and TE Assays Using ACP-Linked Substrates
The ST and TE assays were performed using R)-1-ACP and (3S)-1-ACP substrates. Typically, for the ST reactions, about 300 μM ACP-linked substrate was added with 2 μM ST and 2 mM PAPS in 50 mM Tris-HCl buffer (pH 7.0). For the TE reactions, about 300 μM ACP-linked substrate was added with 2 μM TE in 50 mM Tris-HCl buffer (pH 7.0). All the reactions were incubated at room temperature, quenched by addition of 10% formic acid, and analyzed by reverse-phase HPLC using Jupiter C4 column. The ACP fractions were collected, lyophilized and analyzed by FTICR-MS and IRMPD. To detect products cleaved from ACP by LC-MS, the reaction mixtures were filtered Microcon YM-10 to remove the enzymes. The samples were loaded onto XBridge C18 column (2.1×150 mm, 3.5 μm, Waters), and LC-MS analysis was performed on a Surveyor HPLC system equipped with a ESI-LTQ mass spectrometer (Thermo Scientific). For the coupled ST-TE reactions, the products were extracted with 2×2 ml hexane and dried under nitrogen prior to GC/MS analysis.
GC/EI-MS Analysis
The samples and authentic standard were analyzed by a 6890N gas chromatograph equipped with a 5973 mass selective quadrupole detector (Agilent). The butylamides were separated on a HP-5MS (Agilent J&W) capillary column (30 m×250 μm×0.25 μm), which was operated with helium-carrier gas and splitless injection. Both the injector and detector temperatures were set as 250° C. After an initial setting at 50° C., the oven temperature was raised to 300° C. at 6° C./min and held for 20 minutes. Total ion chromatograms were recorded using a mass range of 60-420 amu, and the selective ion chromatograms were recorded by monitoring the two to three most abundant masses plus the parent masses of target compounds.
Analysis of ACP Samples by Electrospray Ionization (ESI)-FTICR-MS
The observed and calculated masses for the ACP samples are listed in Table 4. Preparation of ACP samples for FTICR-MS analysis was performed as previously described in Gu, et al., Science, 318:970-974 (2007) All samples were analyzed with an actively shielded 7 Tesla quadrupole-FTICR mass spectrometer (APEX-Q, Bruker Daltonics). Target analytes in electrospray solution (1:1 CH3CN:H2O with 0.1% HCOOH) were directly infused into an electrospray ionization (ESI) source (Apollo II, Bruker Daltonics) operating in positive ion mode at a flow rate of 70 μL/h and a voltage of −3.8 kV. A counterflow of hot (240° C.) nitrogen gas was applied to assist desolvation of ESI droplets. Multiply protonated ions generated by ESI were externally accumulated in a hexapole and transferred via high voltage ion optics to the ICR cell for analysis. For IRMPD, precursor ions were mass-selectively accumulated in the hexapole with a 5-10 m/z quadrupole isolation window, transferred to the ICR cell, and irradiated for 100-200 ms by 10.6 μm photons at 10 W laser power, (25 W CO2 laser, Synrad). All data were acquired with XMASS software (version 6.1, Bruker Daltonics) in broadband mode from m/z=200 to 2000 with 512 k data points and summed over 10-30 scans. Mass spectra were analyzed with the MIDAS analysis software. For accurate mass determination, ubiquitin (Sigma) peaks on charge state of 10-11 (ubiquitin was spiked into the ESI solution prior to analysis) was used as internal calibrants to determine the mass of apo-ACP. Once the exact mass of apo-ACP had been determined, its 11 and 13 charge states were selected as external standards for further calibration (ubiquitin was not spiked into all reactions). All frequency-to-m/z calibrations were performed with a two-term calibration equation.
TABLE 4
ESI-FTICR-MS
IRMPD (PEP)
Obs.
Calc.
Obs.
Calc.
ACPII samples
avg mass¶
avg mass¶
[M + H]+
[M + H]+
ACP-SH
13786.92
13786.88
261.134
261.127
1-ACP
14043.01
14043.08
517.349
517.331
2-ACP
14122.99
14123.04
517.349*
517.331*
PEP, Phosphopantetheine ejection product.
¶The ACP species with the N-terminal methionine.
*A same PEP product was observed for 2-ACP and 1-ACP due to laser-induced dissociation of the sulfate group on 2-ACP.
Cloning, Site-Directed Mutagenesis, and Protein Expression
Inserts for CurM ACP (residues 1514-1592), ST (residues 1598-1917) and TE (residues 1929-2211) were generated by polymerase chain reaction amplification from the cosmid pLM14 (28). ACP and ST were inserted into pMCSG7 (29) and TE into pMoCR (30), containing the fusion Mocr to enhance solubility. All constructs were verified by DNA sequencing. The plasmids were transformed into BL21(DE3) E. coli cells and grown at 37° C. in 500 mL TB with 4% glycerol in 2 L baffle flasks until an OD600 of 1.0. Trace metals (50 μM FeCl3, 20 μM CaCl3, 10 μM MnCl2, 10 μM ZnSO4, 2 μM CoCl2, 2 μM CuCl2, 2 μM NiCl2, 2 μM Na2MoO4, 2 μM Na2SeO3, 2 μM H3BO3) were added when growing the ACP. The temperature was lowered to 18° C. and IPTG was added to a final concentration of 0.2 mM. The culture grew for an additional 18 hours, the cells were harvested by centrifugation, and frozen at −20° C. Selenomethionyl (SeMet) protein was produce in BL21(DE3) in SelenoMet™ Medium (AthenaES) containing 100 μg/mL seleno-DL-methionine. Site directed mutagenesis was performed using the QuickChange protocol (Stratagene) and confirmed by DNA sequencing.
Protein Purification
Performing all steps at 4° C. unless noted, the cell pellet from 500 mL of cell culture was re-suspended in 40 mL Buffer A (20 mM Tris pH 7.9, 500 mM NaCl, 20 mM imidazole, and 10% glycerol). DNase (2 mg), lysozyme (5 mg), and MgCl2 (4 mM final concentration) were added and incubated for 30 min. The cells were lysed by sonication and the lysate cleared by centrifugation. The supernatant was filtered through 0.45 μm filters and loaded onto a 5 mL HisTrap Ni NTA resin column (GE Healthcare). The column was washed with 8 column volumes Buffer A. The proteins eluted around 150 mM imidazole by a linear gradient up to 650 mM imidazole (Buffer B). The 6× His-Mocr fusion on the TE was removed by incubating the pooled fractions with 1 mM DTT and 2% (w/w) tobacco etch virus (TEV) protease for two hours at room temperature. The imidazole was removed by dialysis overnight at 4° C. in Buffer C (20 mM Tris pH 7.9, 500 mM NaCl, 10% glycerol) with 1 mM DTT. The reaction mixture was loaded again on the HisTrap column and the flow-through fractions were collected and pooled. All proteins were further purified by size exclusion chromatography with a HiLoad 16/60 Superdex 200 (GE Healthcare) pre-equilibrated with Buffer C. Fractions were pooled and concentrated to 5 mg/mL, flash frozen in liquid N2, and stored at −80° C. The SeMet derivative of the TE was purified as described above with 2 mM DTT added to all buffers. 500 mL of culture yielded 5 mg of purified TE, 2 mg of SeMet TE, 10 mg of ACP, and 20 mg of ST.
Crystallization
Crystals of CurM TE were grown at 4° C. within 24-48 hours in hanging drops using the vapor diffusion method. Protein solution containing 2 mg/mL protein, 20 mM Tris pH 7.9, 200 mM NaCl and 2.5% glycerol was mixed in equal volumes with well solution containing 27-32% PEG3350, 100 mM Tris pH 8.3-8.5. Micro-seeding from native crystals was required for crystal growth of the SeMet protein in similar conditions. Crystals were transferred into cryo protection solution containing well solution with 15% glycerol, harvested in loops and flash frozen in liquid N2.
Data Collection and Structure Determination
Data were collected at GM/CA-CAT beamline 23ID-D at the Advanced Photon Source (APS) at Argonne National Lab (Argonne, Ill.). Among 25 SeMet TE crystals, only one diffracted beyond 4 Å, but had multiple lattices in the diffraction and two distinct crystals. A region visually identified as a single crystal was probed in three 10-μm steps using a 20-μm mini-beam (31). The center position was chosen for the best diffraction with the least interference from the second lattice, and data were collected in inverse-beam geometry (φ=0°-90° and 180°-270° as wedges of 45° with 1° images). The diffraction images showed significant radiation damage, so a different region of the sample was probed in a perpendicular orientation. The crystal was rotate 90° from the initial raster and now looking into the loop, visual identification of a region with a single crystal was impossible. Two separate regions in this orientation were rastered in 3 by 3 boxes in steps of 10-μm with the 10-μm collimator. From these rasters, a single lattice position was identified where data were collected again in inverse beam geometry (φ=90°-150° and 270°-330° as 30° wedges with 0.5° images). The two partial datasets were indexed separately resulting in similar unit cell constants and scaled together, all using the HKL2000 suite (32), to yield a complete SAD dataset. The SeMet TE structure was solved using SOLVE/RESOLVE (33, 34) in the PHENIX software suite. 28 Se sites were found (average figure of merit (FOM)=0.401). After density modification and fourfold noncrystallographic symmetry averaging in RESOLVE the figure of merit was 0.81. AUTOBUILD (35) was used to build an 86% complete initial model, which was completed manually in COOT (36). REFMAC5, from the CCP4 suite, was used for refinement with TLS (37-39).
Sequence Alignment, Structure Alignment and Substrate Modeling
Similar ACP-ST-TE sequences were identified by a BLAST search into the NCBI protein database. ClustalW was used to perform the multiple sequence alignment (40). Pymol was used to align structures and to prepare structure illustrations (41). CurM TE was aligned with affinity labeled PikTE (PDB code 2H7X, RMS=3.309) by superposition of the core domains (residues 55-176 and 232-292 in PikTE to residues 1-126 and 217-282 in CurTE). The PRODRG2 server (42) was used to generate initial atomic coordinates and a topology file for the predicted tetrahedral intermediate. The intermediate was modeled using the affinity label in the active site of PikTE (PDB code 2H7X) (25, 26) as a guide.
Preparation of Substrate-Loaded ACP
The substrate-loaded ACP was prepared by loading 3-hydroxy-5-methoxytetradecanoyl-CoA (28) onto the apo ACP using S. verticillus Svp(43). 50 μM ACP and 100 μM 3-hydroxy-5-methoxytetradecanoyl-CoA were incubated with 10 μM Svp and 10 mM MgCl2 in 100 mM Tris pH 7.9 at 30° C. for 2 hours. The reaction was exchanged into Buffer C, concentrated to 550 μM ACP using Amicon Ultra 10 kDa concentrators (Millipore), flash frozen in 20 μL aliquots, and stored at −80° C. Loading efficiency was analyzed by HPLC using the protocol described in the activity assay.
Activity Assay
TE activity was assayed using a modification of the protocol developed by Gu et. al. (28). To generate the sulfated substrate for the TE assay, 225 μM loaded ACP was incubated with 5 μM ST, 1.75 mM PAPS (Sigma), in 100 mM Tris pH 7.9 at room temperature for 10 min. Four μM TE was then added to the mixture and the reaction was quenched with 10% formic acid after 1 min. The samples were analyzed by reverse phase HPLC using a Jupiter C4 column (250×2.0 mm, 5 μm, 300 Å, Phenomenex) and a linear elution gradient from 30% to 90% CH3CN (0.1% CF3CO2H)/H2O (0.1% CF3CO2H) over 45 min.
Additional features and variations of the invention will be apparent to those skilled in the art from the entirety of this application, including the detailed description, and all such features are intended as aspects of the invention. Likewise, features of the invention described herein can be re-combined into additional embodiments that also are intended as aspects of the invention, irrespective of whether the combination of features is specifically mentioned above as an aspect or embodiment of the invention. Also, only such limitations which are described herein as critical to the invention should be viewed as such; variations of the invention lacking limitations which have not been described herein as critical are intended as aspects of the invention.
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Sherman, David H., Smith, Janet L., Gu, Liangcai, Gehret, Jennifer
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